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EVOGENO Report Summary

Project ID: 310482
Funded under: FP7-IDEAS-ERC
Country: United Kingdom

Mid-Term Report Summary - EVOGENO (Dissecting the genetic basis of divergent and convergent evolution: From individuals to species radiations)

EVOGENO aims to dissect the genetic basis of evolutionary adaptive divergence and the related issue of how new species form. The project comprises three parts: (1) to identify genes under convergent and divergent selection associated with the origins and diversification of echolocation and dietary specialisations in bats, (2) to identify loci under selection in the earliest stages of speciation, and (3), to identify loci underpinning mate choice in horseshoe bats.

To address (1) we have focused our efforts on collecting and analysing genome-wide sequence data from a large number of New World leaf-nosed bats (Phyllostomidae), which show unparalleled diversification linked to dietary specialisation. To this end, we have developed a high-throughput bioinformatics pipeline to conduct a genome-wide scan for accelerated substitutions and molecular adaptation in dietary genes across the Phyllostomidae, and bats as a whole. From our material, we have produced alignments of approximately 15,000 orthologous genes for ~60 species; this is the largest comparative genomic dataset of bats of its kind and one of the largest for any mammal group. Analyses of this dataset by PhD student Potter, with input from others in the team, have found evidence of positive selection in multiple loci that are putatively linked to the adaptive radiation of diet, including two genes implicated in facial development. Gene ontology analysis reveals significant enrichment in biological processes related to carboxylic acid and lipid metabolism. We are in the process of writing up these findings.

Also for part (1), specifically to address molecular adaptations associated with echolocation, we have analysed genome data from two groups: the mustached bats (family Mormoopidae) and also cetaceans. The mustached bats show multiple types of echolocation and thus offer a promising group in which to find “echolocation genes”. PhD student Kim Warren has collected transcriptome datasets for most species in this family, and is currently analysing the results. In terms of cetaceans, we have obtained published genome data from both non-echolocating and echolocating forms, and we have also collected our own transcriptome data from the humpback whale, as well as the hippopotamus; the latter taxon is important because it is the closest extant relative of the cetaceans. By comparing these taxa, we were able to identify molecular adaptations that arose after cetaceans entered the water. We identified >11,000 orthologous genes and compiled a genome-wide dataset of 6,845 coding DNA sequences across 23 mammals (including a total of 9 cetaceans). By combining evidence of positive selection, GO enrichment and protein-protein interactions we found little support for shared ancestral adaptations in the two taxa; and concluded most molecular adaptations in extant cetaceans occurred after their split with hippopotamids (Tsagkogeorga et al, R. Soc. Open Sci., submitted in 2015). We also (as mentioned in the original proposal) sought to test for convergent molecular evolution in mammals more widely. For this we obtained RNA-seq datasets for multiple lineages of subterranean mammals, including 7 African mole-rats, 1 East African spalacid and 1 golden mole species. Using these data, along with published data, we constructed alignments for >8,000 protein coding genes. Screens for positive selection, convergence, and GO enrichment, suggest that the switch to life underground among these different groups has involved functionally similar loci. A manuscript documenting these findings is currently in preparation. Analyses of sequence data from this study have resulted in several papers including the first family-wide molecular evolution study of African mole-rats (Davies et al, MBE accepted) and a candidate gene study of growth hormone and insulin-like growth factor 1 receptors (Davies et al 2014, Gene 549: 228–236).

Associated with parts II and III of the project aims we have improved the genome assembly and annotation of the greater horseshoe bat, Rhinolophus ferrumequinum. This was achieved by combining existing Illumina short read data [previously generated by the group (Tsagkogeorga et al, Curr. Biol. 2013)] with additional genome data from the same individual. Finally, for part II, PhD student Kim Warren is currently engaged in sequencing horseshoe bats that show evidence of having undergone incipient speciation.

In addition, to the previously stated proposal aims, we are also looking for evidence of divergence at the level of gene family evolution. For this, we have assessed the average turnover of gene gain and loss in bats compared to other mammals. Our early results suggest that the number of protein coding genes in bat genomes is highly plastic, and that gains and losses tend to occur in gene families implicated in biological regulation, metabolism and responses to stimuli. Finally, we find evidence that bats have undergone significant gene loss in their Olfactory Receptor (OR) genes. These findings are being prepared for publication. Finally, we have also started to test for divergence and convergence at the level of gene expression, focusing on sensory and dietary tissues of phyllostomid bats. These studies are in their early stages, but preliminary findings from a comparative analysis of eye transcriptomes suggests bats that have evolved frugivory and nectarivory show increased expression in loci associated with lens size.

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United Kingdom
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